The invention discloses a super-hydrophobic chip for enrichment and condensation of molecules as well as a preparation method and an application thereof. The preparation method comprises the following steps: tackifying treatment of a silicon chip which is cleaned is carried out, photoresist is uniformly glued on a silicon chip, and baking is carried out; pre-positioning of the baked silicon chip is carried out for a pattern on a photoetching board and automatic para-position operation is carried out, after pre-positioning is carried out, exposure treatment is carried out, developing treatment is carried out, deep silicon etching treatment is carried out for the silicon chip, crystal film Au is injected on the silicon chip with a silicon column array structure by magnetron sputtering, in order to obtain a template material; graphite which is cleaned is used as a cathode, the template material is used as an anode, the cathode and the anode are placed in an electrodeposition solution in order to obtain a chip with a nanometer silver silicon column array structure, the chip is taken out and cleaned with clear water, and pure argon is used for blowing and drying. The super-hydrophobic chip for enrichment and condensation of molecules has the advantages of hypersensitiveness, fast response, and low loss rate of solvents.